Hyeshik Chang hyeshik

## README.md

      
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    SNU Bioinformatics and Practice 2 - Week 2

Contains the notebooks for the practice sessions.

  
## KNUE-20190510-Slides.pdf

      
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                파이썬으로 하는 데이터 분석: 일상에서 배우기
              
          
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## WASET abstract database processing.ipynb

      
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                Processes the downloaded WASET database to generate tables of Korean authors and abstracts
              
          
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## download-waset.py
#!/usr/bin/env python3
#
# Copyright (c) 2018 Hyeshik Chang
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:

## 0524 Bamtori NIPT Interpretation.ipynb

      
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                hyeshik
                / 0524 Bamtori NIPT Interpretation.ipynb
            
            
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              June 19, 2016 15:38
            
          
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## 0609 Mad Scienctist Generator.ipynb

      
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                hyeshik
                / 0609 Mad Scienctist Generator.ipynb
            
            
              Created
              June 10, 2016 09:41
            
          
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## 1226 Burger Index.ipynb.json
{
 "metadata": {
  "name": "",
  "signature": "sha256:f99925a6f73a1e36bc91415d84266705e3bdf72304d8dba7bcfb6c94ca7b270a"
 },
 "nbformat": 3,
 "nbformat_minor": 0,
 "worksheets": [
  {
   "cells": [

## Citation trends 2013.ipynb.json
{
 "metadata": {
  "name": "",
  "signature": "sha256:d1355cd3916fec7cb8d44c23a9217f3bbff36499b973ea66c47448aa35736365"
 },
 "nbformat": 3,
 "nbformat_minor": 0,
 "worksheets": [
  {
   "cells": [

## jobscript.sh
#!/bin/sh
#rule: {job}
#input: {job.input}
#output: {job.output}
#threads: {job.threads}
{self.workflow.snakemakepath} --snakefile {self.workflow.snakefile} \
--force -j{self.cores} \
--directory {workdir} --nocolor --notemp --quiet --nolock {job.output} \
> /dev/null && touch "{jobfinished}" || touch "{jobfailed}"
exit 0

## sgesnake.sh
#!/bin/sh
#
# Adopts and submit a snakemake cluster job script to SGE queue
#
#  by Hyeshik Chang
#

JOBSCRIPT_SNAKEMAKE=$1
JOBSCRIPT_SGE="`dirname $1`/sge`basename $1`"
	#!/usr/bin/env python3
	#
	# Copyright (c) 2018 Hyeshik Chang
	#
	# Permission is hereby granted, free of charge, to any person obtaining a copy
	# of this software and associated documentation files (the "Software"), to deal
	# in the Software without restriction, including without limitation the rights
	# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
	# copies of the Software, and to permit persons to whom the Software is
	# furnished to do so, subject to the following conditions:
	{
	"metadata": {
	"name": "",
	"signature": "sha256:f99925a6f73a1e36bc91415d84266705e3bdf72304d8dba7bcfb6c94ca7b270a"
	},
	"nbformat": 3,
	"nbformat_minor": 0,
	"worksheets": [
	{
	"cells": [
	{
	"metadata": {
	"name": "",
	"signature": "sha256:d1355cd3916fec7cb8d44c23a9217f3bbff36499b973ea66c47448aa35736365"
	},
	"nbformat": 3,
	"nbformat_minor": 0,
	"worksheets": [
	{
	"cells": [
	#!/bin/sh
	#rule: {job}
	#input: {job.input}
	#output: {job.output}
	#threads: {job.threads}
	{self.workflow.snakemakepath} --snakefile {self.workflow.snakefile} \
	--force -j{self.cores} \
	--directory {workdir} --nocolor --notemp --quiet --nolock {job.output} \
	> /dev/null && touch "{jobfinished}" \|\| touch "{jobfailed}"
	exit 0
	#!/bin/sh
	#
	# Adopts and submit a snakemake cluster job script to SGE queue
	#
	# by Hyeshik Chang
	#

	JOBSCRIPT_SNAKEMAKE=$1
	JOBSCRIPT_SGE="`dirname $1`/sge`basename $1`"